Fixed in version 0.4.4. You can specify an own highlighting class with --highlighter/-h
See a dummy geshi highlighter:
http://tmp.cweiske.de/PhD_Highlighter_Geshi.phps
One would put it into PhD/Highlighter/Geshi.php, so that it is in the include path, and specify "-h PhD_Highlighter_Geshi" to phd on cmdline.